Data from: Phylogeographic and cross-species transmission dynamics of SAT1 and SAT2 Foot-and-Mouth Disease Virus in Eastern Africa

Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programs in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyze SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (P=0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (P=0.72). Salient (Bayes Factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities SAT1 Host BEAST FileBEAST data and priors for running a discrete trait model for host species transmission of FMD SAT1 in East AfricaSAT1_Discrete_Host_Asymmteric_BEAST.xmlSAT1 BEAST phylogeographic fileBEAST data and priors for running a discrete trait model for geographic transmission of FMD SAT1 in East AfricaSAT1_Phylogeographic_Asymmteric_BEAST.xmlSAT2 Host BEAST fileContains data and prior for running a discrete trait model for host transmission of FMD SAT2 in east AfricaSAT2_Discrete_Host_Asymmteric_BEAST.xmlSAT2 Phylogeography BEAST fileContains data and prior for running a discrete trait model for phylogeography of FMD SAT2 in east AfricaSAT2_Phylogeographic_Asymmteric_BEAST.xmlSAT1 sequences fileContains sequences and their Genbank accession numbers used in the phylodynamic analysesSAT1.nexSAT2 sequences fileContains sequences and their Genbank accession numbers used in the phylodynamic analysesSAT2.nexSAT1 host MCC tree fileContains the summarized maximum clade credibility tree file for the host transmission of FMD SAT1 in East AfricaSAT1_Discrete_Host_Asymmteric_MCC.treSAT1 phylogeography MCC tree fileContains the summarized maximum clade credibility tree file for the phylogeography of FMD SAT1 in East AfricaSAT1_Phylogeographic_Asymmteric_MCC.treSAT2 phylogeography MCC tree fileContains the summarized Maximum clade credibility tree for the phylogeography of FMD SAT2 in East AfricaSAT2_Phylogeographic_Asymmteric_MCC.tre